Package: sRACIPE
Type: Package
Title: Systems biology tool to simulate gene regulatory circuits
Version: 2.2.0
Authors@R: c(
    person("Mingyang", "Lu", , "m.lu@northeastern.edu", role = c("aut", "cre"), 
      comment = c(ORCID = "0000-0001-8158-0593")
    ),
    person("Vivek", "Kohar", role = "aut"
    ),
    person("Aidan", "Tillman", role = "aut"
    ),
    person("Daniel", "Ramirez", role = "aut")
    )
Description: sRACIPE implements a randomization-based method for gene
        circuit modeling. It allows us to study the effect of both the
        gene expression noise and the parametric variation on any gene
        regulatory circuit (GRC) using only its topology, and simulates
        an ensemble of models with random kinetic parameters at
        multiple noise levels. Statistical analysis of the generated
        gene expressions reveals the basin of attraction and stability
        of various phenotypic states and their changes associated with
        intrinsic and extrinsic noises. sRACIPE provides a holistic
        picture to evaluate the effects of both the stochastic nature
        of cellular processes and the parametric variation.
License: MIT + file LICENSE
Encoding: UTF-8
Suggests: knitr, BiocStyle, rmarkdown, tinytest
VignetteBuilder: knitr
LinkingTo: Rcpp
biocViews: ResearchField, SystemsBiology, MathematicalBiology,
        GeneExpression, GeneRegulation, GeneTarget
Depends: R (>= 3.6.0),SummarizedExperiment, methods, Rcpp
Imports: ggplot2, reshape2, MASS, RColorBrewer, gridExtra,visNetwork,
        gplots, umap, htmlwidgets, S4Vectors, BiocGenerics, grDevices,
        stats, utils, graphics, doFuture, doRNG, future, foreach
RoxygenNote: 7.3.2
URL: https://github.com/lusystemsbio/sRACIPE, https://geneex.jax.org/,
        https://vivekkohar.github.io/sRACIPE/
BugReport: https://github.com/lusystemsbio/sRACIPE/issues
LazyData: true
Config/pak/sysreqs: make libicu-dev libpng-dev libssl-dev python3
        zlib1g-dev
Repository: https://bioc-release.r-universe.dev
Date/Publication: 2025-10-29 14:51:28 UTC
RemoteUrl: https://github.com/bioc/sRACIPE
RemoteRef: RELEASE_3_22
RemoteSha: 26d0307b96b871af312c4f7dffe3af7f905c0361
NeedsCompilation: yes
Packaged: 2026-03-02 08:45:09 UTC; root
Author: Mingyang Lu [aut, cre] (ORCID: <https://orcid.org/0000-0001-8158-0593>),
  Vivek Kohar [aut],
  Aidan Tillman [aut],
  Daniel Ramirez [aut]
Maintainer: Mingyang Lu <m.lu@northeastern.edu>
Built: R 4.5.2; x86_64-w64-mingw32; 2026-03-02 08:47:12 UTC; windows
Archs: x64
